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Description
In this tutorial, we will show how to use containers and submit jobs to an HPC cluster farm using udocker. The tutorial will be online via Zoom.
We will show this for a "Gromacs" container and for a "Tensorflow" using GPUs.
It's recommended to have some knowledge of using and submitting jobs to an HPC cluster. No previous knowledge of containers is required.
Optional preparation
If you want to compile gromacs yourself, to be used later with udocker
Install docker engine in your laptop or desktop (if you haven't done so already), and do the following:
$ git clone https://github.com/mariojmdavid/docker-gromacs-cuda.git
$ cd docker-gromacs-cuda/gromacs-cpu/
$ docker build --build-arg gromacs_ver=2025.4 -t gromacs-openmp-2005.4 -f Dockerfile-cpu .
(Will take quite awhile, 30 minutes on my desktop)
Check if the image was built, and save that image as a tarball
$ docker images
$ docker save -o gromacs.tar gromacs-openmp-2005.4
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